1-203184506-C-G

Position:

• chr1-203184506-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001276.4(CHI3L1):​c.314+70G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,281,154 control chromosomes in the GnomAD database, including 157,584 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (14582 hom., cov: 31)
  • Exomes 𝑓: 0.50 (143002 hom.)
• Consequence: CHI3L1 NM_001276.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

Genes affected

CHI3L1 (HGNC:1932): (chitinase 3 like 1) Chitinases catalyze the hydrolysis of chitin, which is an abundant glycopolymer found in insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 family of chitinases includes eight human family members. This gene encodes a glycoprotein member of the glycosyl hydrolase 18 family. The protein lacks chitinase activity and is secreted by activated macrophages, chondrocytes, neutrophils and synovial cells. The protein is thought to play a role in the process of inflammation and tissue remodeling. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHI3L1	NM_001276.4	c.314+70G>C		intron_variant		ENST00000255409.8	NP_001267.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHI3L1	ENST00000255409.8	c.314+70G>C		intron_variant		1	NM_001276.4	ENSP00000255409.3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63436 AN: 151796 Hom.: 14578 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.497 AC: 561044 AN: 1129240 Hom.: 143002 AF XY: 0.498 AC XY: 287172 AN XY: 576902

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.274

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.346

Gnomad4 SAS exome AF: 0.470

Gnomad4 FIN exome AF: 0.545

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.467

GnomAD4 genome AF: 0.418 AC: 63465 AN: 151914 Hom.: 14582 Cov.: 31 AF XY: 0.419 AC XY: 31085 AN XY: 74250

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.419

Alfa AF: 0.329 Hom.: 944

Bravo AF: 0.389

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2071579; hg19: chr1-203153634; COSMIC: COSV55137927; COSMIC: COSV55137927;